3IWA | pdb_00003iwa

Crystal structure of a FAD-dependent pyridine nucleotide-disulphide oxidoreductase from Desulfovibrio vulgaris

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	294	100mM sodium cacodylate pH 5.5, 8% PEG 8K, 200mM calcium acetate, vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.564	α = 90
b = 127.564	β = 90
c = 157.713	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2009-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.3	32.09	99.8	0.103	0.103	12.2	7.3	22125	22081			38.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	100		0.373	0.373	4.8	7.2	3190

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.3	20	22086	22046	1130	99.82	0.21	0.208	0.21	0.243	0.25	RANDOM	47.86

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.82	0.91		1.82		-2.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.723
r_dihedral_angle_4_deg	21.628
r_dihedral_angle_3_deg	15.756
r_dihedral_angle_1_deg	6.301
r_scangle_it	3.778
r_scbond_it	2.337
r_mcangle_it	1.723
r_angle_refined_deg	1.485
r_angle_other_deg	0.93
r_mcbond_it	0.918

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.723
r_dihedral_angle_4_deg	21.628
r_dihedral_angle_3_deg	15.756
r_dihedral_angle_1_deg	6.301
r_scangle_it	3.778
r_scbond_it	2.337
r_mcangle_it	1.723
r_angle_refined_deg	1.485
r_angle_other_deg	0.93
r_mcbond_it	0.918
r_mcbond_other	0.151
r_chiral_restr	0.082
r_bond_refined_d	0.015
r_bond_other_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2900
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	1

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.